ImageData-class {Cardinal} | R Documentation |
A container class for holding imaging data, designed to contain one or more arrays in an immutable environment. It is assumed that the first dimension of each array corresponds to the features.
Note that only visible objects (names not beginning with '.') are checked for validity; however, all objects are copied if any elements in the data
slot are modified when data
is an "immutableEnvironment".
## Instance creation ImageData(..., data = new.env(parent=emptyenv()), storageMode = c("immutableEnvironment", "lockedEnvironment", "environment")) ## Additional methods documented below
... |
Named arguments that are passed to the |
data |
An environment in which to assign the previously named variables. |
storageMode |
The storage mode to use for the |
data
:An environment
which may contain one or more arrays with an equal number of dimensions. It is assumed that the first dimension corresponds to the features.
storageMode
:A character
which is one of "immutableEnvironment"
, "lockedEnvironment"
, or "environment"
. The values "lockedEnvironment"
and "environment"
behave as described in the documentation of AssayData
. An "immutableEnvironment"
uses a locked environment while retaining R's typical copy-on-write behavior. Whenever an object in an immutable environment is modified, a new environment is created for the data
slot, and all objects copied into it. This allows usual R functional semantics while avoiding copying of large objects when other slots are modified.
.__classVersion__
:A Versions
object describing the version of the class used to created the instance. Intended for developer use.
ImageData
instances are usually created through ImageData()
.
Class-specific methods:
storageMode(object)
, storageMode(object)<-
:Return or set the storage mode. See documentation on the storageMode
slot above for more details.
Standard generic methods:
initialize
:Initialize an ImageData
object. Called by new
. Not to be used by the user.
validObject
:Validity-check that the arrays in the data
slot environment are all of equal number of dimensions, and the storage mode is a valid value.
combine(x, y, ...)
:Combine two or more ImageData
objects. All elements must have matching names, and are combined with calls to combine
. Higher dimensional arrays are combined using the same rules as for matrices. (See combine
for more details.)
annotatedDataFrameFrom(object)
:Returns an IAnnotatedDataFrame
with columns for the dimensions of the elements of data
. All dimensions must be named (determined by the rownames(dims(object))
). It is assumed that the first dimension corresponds to the features, and is not used as a dimension in the returned IAnnotatedDataFrame
. Additional arguments (byrow
, ...) are ignored.
dims
:A matrix with each column corresponding to the dimensions of an element in the data
slot.
names(x)
, names(x)<-
:Access or replace the array names of the elements contained in the data
slot environment.
ImageData[[name]]
, ImageData[[name]] <- value
:Access or replace an element named "name"
in the environment in the data
slot.
Kylie A. Bemis
AssayData
,
SImageData
,
SImageSet
,
MSImageSet
## Create an ImageData object ImageData() idata <- ImageData(data0=matrix(1:4, nrow=2)) idata[["data0"]] # Immutable environments in ImageData objects storageMode(idata) <- "lockedEnvironment" try(idata[["data0"]][,1] <- c(10,11)) # Fails storageMode(idata) <- "immutableEnvironment" try(idata[["data0"]][,1] <- c(10,11)) # Succeeds # Test copy-on-write for immutable environments idata2 <- idata idata2[["data0"]] <- matrix(5:8, nrow=2) idata[["data0"]] == idata2[["data0"]] # False